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In each episode, Tom (live-acted) comes out of his house's back door, puts on a power belt, and runs across his lawn into a woodland, barely clearing a bike laid on the grass. In there is the tree with Treetopolis on, protected by a magic shield. Using the power belt he performs some Tree Fu moves, jumps up, shrinks to insect size as he flies into the tree, and enters the world of Treetopolis, where he has adventures. He is skilled in that world's magic, and often gets characters out of scrapes. The tree's sap is shown as a glowing orange magic liquid.

At least twice in each episode, Tom has to call on "the big world" for magical help: breaking the fourthwall, he asks the audience to make magical moves and say magical words to assist the necessary magical actions. The magical power is shown as an orange glow that appears offscreen and flies towards at Tom, who collects it in his arms as a ball of energy, and uses it to complete thespell.

The movements which the audience are called on to make are particularly beneficial for the development of children with developmental coordination disorder.

Thescenario includes magical hoverboards (called "leaf boards"), a sport called "Squizzle" and lots of different cakes and snacks that the inhabitants of Treetopolis like to eat! The characters occasionally communicate via a small, yellow, glowing device called a Holopax, in which they can see the miniature translucent form of their interlocutor.Characters also use a variety of small electronic devices to access various Wiki services (including "Fungopedia") to learn more about the plant and animal life around them.

At the end of each episode, Tom says, "Well, guys, it's time for me to head home. Bye everyone!" and he wishes his friends, and they shouted, "Bye, Tom!" Then he wave goodbye and flies up, and out of the tree's magic field. Back in the normal world, Then tom says to the viewers as he flies up, "Thanks for helping me in Treetopolis. See you soon for another adventure! Bye, for now!" and he reverts to a human boy, lands, runs outof the wood and across his back lawn, jumping over a bicycle lying on the lawn, and in through his back door.

The series's two main voice actors each previously played major roles in Doctor Who; Sophie Aldred (who voices the animated Tom) as Seventh Doctor companion Ace and David Tennant (who voices Twigs) as the Tenth Doctor. The actor who plays Tom in the live action opening and closing sections of the show, Adam Henderson, is Sophie Aldred's son.